After posting losing records in their first four seasons, the team finished second behind the Hokkaido Nippon-Ham Fighters in the 2009 pennant race under the leadership of manager Katsuya Nomura, the oldest manager in NPB history. In the league championship playoffs the Eagles lost the six-game series against the Fighters 1–4 and Nomura announced his retirement. In 2010 the team was managed by American Marty Brown, the former manager of the Hiroshima Toyo Carp. Brown was fired after a single season after the team had slumped back to last place. Hall of Fame member Senichi Hoshino subsequently managed the team for four years, including their successful 2013 season, where they defeated the Chiba Lotte Marines to claim the League championship and went on to become Japan Series champions after defeating the Yomiuri Giants. Masataka Nashida has been the team's manager since 2016.

10 – This number is worn by both team mascots, Clutch and Clutchina, and is considered the number of the fan, the 'tenth man' on the field. It is the first retired number in NPB involving a fan, inspired by some teams in other sports (such as football, which retires "12" for the "12th man", or basketball, which retires "6" for the "6th man"). There are ten starting players in the Pacific League as the league uses the designated hitter. The Chiba Lotte Marines has the No. 26 retired in similar fashion (MLB's Los Angeles Angels of Anaheim has retired No. 26, in similar fashion, for the original owner Gene Autry).